SMTL ID : 4fjm.1

RB69 DNA polymerase ternary complex with dCTP/dA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 18 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, P.417, R.482, K.486, K.560, N.564, T.622, D.623 Chain B: A.3, G.4 Chain C: C.13 Ligands: CA.2, CA.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:L.412, A:S.414, A:L.415, A:Y.416, A:N.564, A:N.564 Water bridges: A:R.482 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DCP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 CA.3: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: DCP.1, CA.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.623, H2O.8 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.2, H2O.6, H2O.14 CA.5: 1 residues within 4Å: Chain A: E.716 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.716, H2O.3, H2O.10, H2O.13 CA.6: 2 residues within 4Å: Chain A: E.116, I.309 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.1, H2O.14, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. J.Am.Chem.Soc. (2013)

Release Date

2012-12-19

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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